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  1. Book: Essentials of medical genomics

    Brown, Stuart M. / Hay, John G. / Ostrer, Harry

    2009  

    Author's details Stuart M. Brown. With contributions by John G. Hay and Harry Ostrer
    Keywords Genetics, Medical ; Genomics ; Genome, Human ; Medical genetics
    Subject code 616.042
    Language English
    Size XII, 439 S. : Ill.
    Edition 2. ed.
    Publisher Wiley-Blackwell
    Publishing place Hoboken, NJ
    Publishing country United States
    Document type Book
    HBZ-ID HT015656580
    ISBN 978-0-470-14019-2 ; 0-470-14019-4
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2008 A 6326 order for loan Magazin

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  2. Book: Next-generation DNA sequencing informatics

    Brown, Stuart M

    2015  

    Abstract: Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making genome and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene ... ...

    Author's details edited by Stuart M. Brown
    Abstract "Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making genome and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene expression, transcription factor analysis, metagenomics, and epigenetics. Bioinformatics methods to support DNA sequencing have become and remain a critical bottleneck for many researchers and organizations wishing to make use of NGS technology. Next-Generation DNA Sequencing Bioinformatics, Second Edition, provides thorough, plain language introduction to the necessary informatics methods and tools for analyzing NGS data as did the first edition, and provides detailed descriptions of algorithms, strengths and weaknesses of specific tools, pitfalls and alternative methods. Four new chapters in this edition cover: experimental design, sample preparation, and quality assessment of NGS data; Public databases for DNA Sequencing data; De novo transcript assembly; proteogenomics; and emerging sequencing technologies. The remaining chapters from the first edition have been updated with the latest information. This book also provides extensive reference to best-practice bioinformatics methods for NGS applications and tutorials for common workflows. The second edition of Next-Generation DNA Sequencing Bioinformatics addresses the informatics needs of students, laboratory scientists, and computing specialists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies"--
    MeSH term(s) Sequence Analysis, DNA ; Computational Biology/methods
    Language English
    Size xiv, 402 pages :, illustrations ;, 27 cm
    Edition Second edition.
    Document type Book
    ISBN 9781621821236 ; 1621821234
    Database Catalogue of the US National Library of Medicine (NLM)

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  3. Book: Next-generation DNA sequencing informatics

    Brown, Stuart M

    2015  

    Abstract: Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making complete genome sequencing an affordable and frequently used tool for a wide variety of research applications. This book provides a thorough introduction to ... ...

    Author's details ed. by Stuart M. Brown
    Abstract "Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making complete genome sequencing an affordable and frequently used tool for a wide variety of research applications. This book provides a thorough introduction to the necessary informatics methods and tools for operating NGS instruments and analyzing NGS data"--

    "Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making genome and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene expression, transcription factor analysis, metagenomics, and epigenetics. Bioinformatics methods to support DNA sequencing have become and remain a critical bottleneck for many researchers and organizations wishing to make use of NGS technology. Next-Generation DNA Sequencing Bioinformatics, Second Edition, provides thorough, plain language introduction to the necessary informatics methods and tools for analyzing NGS data as did the first edition, and provides detailed descriptions of algorithms, strengths and weaknesses of specific tools, pitfalls and alternative methods. Four new chapters in this edition cover: experimental design, sample preparation, and quality assessment of NGS data; Public databases for DNA Sequencing data; De novo transcript assembly; proteogenomics; and emerging sequencing technologies. The remaining chapters from the first edition have been updated with the latest information. This book also provides extensive reference to best-practice bioinformatics methods for NGS applications and tutorials for common workflows. The second edition of Next-Generation DNA Sequencing Bioinformatics addresses the informatics needs of students, laboratory scientists, and computing specialists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies"--

    Literaturangaben
    Keywords Bioinformatics ; Nucleotide sequence
    Language English
    Size 350 S., Ill., graph. Darst.
    Edition 2. ed.
    Publisher Cold Spring Harbor Laboratory Press
    Publishing place Cold Spring Harbor, NY
    Document type Book
    ISBN 9781621821236 ; 1621821234
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  4. Book: Next-generation DNA sequencing informatics

    Brown, Stuart M

    2013  

    Title variant NGS
    Author's details ed. by Stuart M. Brown
    Keywords Bioinformatics ; Nucleotide sequence
    Language English
    Size XIII, 241 S., Ill., graph. Darst.
    Publisher CSH Press, Cold Spring Harbor Laboratory Press
    Publishing place Cold Spring Harbor, NY
    Document type Book
    Note Literaturangaben
    ISBN 9781936113873 ; 1936113872
    Database Leibniz Institute of Plant Genetics and Crop Plant Research

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  5. Book: Next-generation DNA sequencing informatics

    Brown, Stuart M

    2013  

    Title variant NGS
    Author's details ed. by Stuart M. Brown
    Keywords Bioinformatics ; Nucleotide sequence
    Language English
    Size XIII, 241 S., Ill., graph. Darst.
    Publisher CSH Press, Cold Spring Harbor Laboratory Press
    Publishing place Cold Spring Harbor, NY
    Document type Book
    Note Literaturangaben
    ISBN 9781936113873 ; 1936113872
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  6. Article ; Online: Author Correction: Parkinson's disease and bacteriophages as its overlooked contributors.

    Tetz, George / Brown, Stuart M / Hao, Yuhan / Tetz, Victor

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 12078

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Language English
    Publishing date 2020-07-16
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-69086-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages.

    Tetz, George / Brown, Stuart M / Hao, Yuhan / Tetz, Victor

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 9685

    Abstract: The etiopathogenesis of type 1 diabetes (T1D), a common autoimmune disorder, is not completely understood. Recent studies suggested the gut microbiome plays a role in T1D. We have used public longitudinal microbiome data from T1D patients to analyze ... ...

    Abstract The etiopathogenesis of type 1 diabetes (T1D), a common autoimmune disorder, is not completely understood. Recent studies suggested the gut microbiome plays a role in T1D. We have used public longitudinal microbiome data from T1D patients to analyze amyloid-producing bacterial composition and found a significant association between initially high amyloid-producing Escherichia coli abundance, subsequent E. coli depletion prior to seroconversion, and T1D development. In children who presented seroconversion or developed T1D, we observed an increase in the E. coli phage/E. coli ratio prior to E. coli depletion, suggesting that the decrease in E. coli was due to prophage activation. Evaluation of the role of phages in amyloid release from E. coli biofilms in vitro suggested an indirect role of the bacterial phages in the modulation of host immunity. This study for the first time suggests that amyloid-producing E. coli, their phages, and bacteria-derived amyloid might be involved in pro-diabetic pathway activation in children at risk for T1D.
    MeSH term(s) Amyloid/metabolism ; Autoimmunity/immunology ; Child, Preschool ; Coliphages/immunology ; Coliphages/metabolism ; Diabetes Mellitus, Type 1/etiology ; Diabetes Mellitus, Type 1/metabolism ; Diabetes Mellitus, Type 1/pathology ; Escherichia coli/immunology ; Escherichia coli/metabolism ; Gastrointestinal Microbiome/immunology ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Prospective Studies
    Chemical Substances Amyloid
    Language English
    Publishing date 2019-07-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-46087-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: CRISPR/Cas9 does not facilitate stable expression of long C9orf72 dipeptides in mice.

    Ryan, Sarah / Hobbs, Eleanor / Rollinson, Sara / Pickering-Brown, Stuart M

    Neurobiology of aging

    2019  Volume 84, Page(s) 235.e1–235.e8

    Abstract: A C9orf72 repeat expansion is the most common cause of both frontotemporal dementia and motor neuron disease. The expansion is translated to produce dipeptide repeat proteins (DPRs), which are toxic in vivo and in vitro. However, the mechanisms ... ...

    Abstract A C9orf72 repeat expansion is the most common cause of both frontotemporal dementia and motor neuron disease. The expansion is translated to produce dipeptide repeat proteins (DPRs), which are toxic in vivo and in vitro. However, the mechanisms underlying DPR toxicity remain unclear. Mouse models which express DPRs at repeat lengths found in human disease are urgently required to investigate this. We aimed to generate transgenic mice expressing DPRs at repeat lengths of >1000 using alternative codon sequences, to reduce the repetitive nature of the insert. We found that although these inserts did integrate into the mouse genome, the alternative codon sequences did not protect from instability between generations. Our findings suggest that stable integration of long DPR sequences may not be possible. Administration of viral vectors after birth may be a more effective delivery method for long repeats.
    MeSH term(s) Animals ; C9orf72 Protein ; Clustered Regularly Interspaced Short Palindromic Repeats ; Mice ; Mice, Transgenic ; Trinucleotide Repeat Expansion
    Chemical Substances C9orf72 Protein ; C9orf72 protein, mouse
    Language English
    Publishing date 2019-09-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 604505-4
    ISSN 1558-1497 ; 0197-4580
    ISSN (online) 1558-1497
    ISSN 0197-4580
    DOI 10.1016/j.neurobiolaging.2019.09.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1685: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 10: Show issues

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  9. Article ; Online: The cellular expression and proteolytic processing of the amyloid precursor protein is independent of TDP-43.

    Hicks, David A / Jones, Alys C / Pickering-Brown, Stuart M / Hooper, Nigel M

    Bioscience reports

    2020  Volume 40, Issue 4

    Abstract: Alzheimer's disease (AD) is a neurodegenerative condition, of which one of the cardinal pathological hallmarks is the extracellular accumulation of amyloid β (Aβ) peptides. These peptides are generated via proteolysis of the amyloid precursor protein ( ... ...

    Abstract Alzheimer's disease (AD) is a neurodegenerative condition, of which one of the cardinal pathological hallmarks is the extracellular accumulation of amyloid β (Aβ) peptides. These peptides are generated via proteolysis of the amyloid precursor protein (APP), in a manner dependent on the β-secretase, BACE1 and the multicomponent γ-secretase complex. Recent data also suggest a contributory role in AD of transactive response DNA binding protein 43 (TDP-43). There is little insight into a possible mechanism linking TDP-43 and APP processing. To this end, we used cultured human neuronal cells to investigate the ability of TDP-43 to interact with APP and modulate its proteolytic processing. Immunocytochemistry showed TDP-43 to be spatially segregated from both the extranuclear APP holoprotein and its nuclear C-terminal fragment. The latter (APP intracellular domain) was shown to predominantly localise to nucleoli, from which TDP-43 was excluded. Furthermore, neither overexpression of each of the APP isoforms nor siRNA-mediated knockdown of APP had any effect on TDP-43 expression. Doxycycline-stimulated overexpression of TDP-43 was explored in an inducible cell line. Overexpression of TDP-43 had no effect on expression of the APP holoprotein, nor any of the key proteins involved in its proteolysis. Furthermore, increased TDP-43 expression had no effect on BACE1 enzymatic activity or immunoreactivity of Aβ1-40, Aβ1-42 or the Aβ1-40:Aβ1-42 ratio. Also, siRNA-mediated knockdown of TDP-43 had no effect on BACE1 immunoreactivity. Taken together, these data indicate that TDP-43 function and/or dysfunction in AD is likely independent from dysregulation of APP expression and proteolytic processing and Aβ generation.
    MeSH term(s) Alzheimer Disease/pathology ; Amyloid Precursor Protein Secretases/metabolism ; Amyloid beta-Protein Precursor/genetics ; Amyloid beta-Protein Precursor/metabolism ; Aspartic Acid Endopeptidases/metabolism ; Cell Line, Tumor ; Cell Nucleus/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Knockdown Techniques ; Humans ; Neurons/cytology ; Neurons/metabolism ; Proteolysis ; RNA, Small Interfering/metabolism
    Chemical Substances APP protein, human ; Amyloid beta-Protein Precursor ; DNA-Binding Proteins ; RNA, Small Interfering ; TARDBP protein, human ; Amyloid Precursor Protein Secretases (EC 3.4.-) ; Aspartic Acid Endopeptidases (EC 3.4.23.-) ; BACE1 protein, human (EC 3.4.23.46)
    Language English
    Publishing date 2020-04-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 764946-0
    ISSN 1573-4935 ; 0144-8463
    ISSN (online) 1573-4935
    ISSN 0144-8463
    DOI 10.1042/BSR20200435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1676: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Parkinson's disease and bacteriophages as its overlooked contributors.

    Tetz, George / Brown, Stuart M / Hao, Yuhan / Tetz, Victor

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 10812

    Abstract: Recent studies suggest that alterations in the gut phagobiota may contribute to pathophysiological processes in mammals; however, the association of bacteriophage community structure with Parkinson's disease (PD) has not been yet characterized. Towards ... ...

    Abstract Recent studies suggest that alterations in the gut phagobiota may contribute to pathophysiological processes in mammals; however, the association of bacteriophage community structure with Parkinson's disease (PD) has not been yet characterized. Towards this end, we used a published dataset to analyse bacteriophage composition and determine the phage/bacteria ratio in faecal samples from drug-naive PD patients and healthy participants. Our analyses revealed significant alterations in the representation of certain bacteriophages in the phagobiota of PD patients. We identified shifts of the phage/bacteria ratio in lactic acid bacteria known to produce dopamine and regulate intestinal permeability, which are major factors implicated in PD pathogenesis. Furthermore, we observed the depletion of Lactococcus spp. in the PD group, which was most likely due to the increase of lytic c2-like and 936-like lactococcal phages frequently present in dairy products. Our findings add bacteriophages to the list of possible factors associated with the development of PD, suggesting that gut phagobiota composition may serve as a diagnostic tool as well as a target for therapeutic intervention, which should be confirmed in further studies. Our results open a discussion on the role of environmental phages and phagobiota composition in health and disease.
    MeSH term(s) Bacteria/genetics ; Bacteria/isolation & purification ; Bacteria/metabolism ; Bacteriophages/genetics ; Bacteriophages/isolation & purification ; Case-Control Studies ; DNA, Bacterial/chemistry ; DNA, Bacterial/isolation & purification ; DNA, Bacterial/metabolism ; DNA, Viral/chemistry ; DNA, Viral/isolation & purification ; DNA, Viral/metabolism ; Dopamine/metabolism ; Feces/microbiology ; Feces/virology ; Humans ; Microbiota ; Parkinson Disease/pathology ; Parkinson Disease/virology ; Principal Component Analysis
    Chemical Substances DNA, Bacterial ; DNA, Viral ; Dopamine (VTD58H1Z2X)
    Language English
    Publishing date 2018-07-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-29173-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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